Project description:Lipomyces genome scale model based on the Lipomyces starkeyi NRRL-11557 genome.
Published in:
Genome-Scale Model Development and Genomic Sequencing of the Oleaginous Clade Lipomyces
Frontiers in Bioengineering and Biotechnology
Industrial Biotechnology
Volume 12 - 2024 | doi: 10.3389/fbioe.2024.1356551
Project description:A maturation, sex and lunar phase locked Platynereis head proteome was generated by sampling six heads per biological replicate from male and female Platynereis at defined stages of sexual maturation (immature, premature and mature) at two different moon phases; New moon and Free-running Full moon, meaning the animals would expect a nocturnal light stimulus, Full moon, which was not given. From these heads RNA and protein were extracted simultaneously and used for both transcriptomics (ENA accession no. PRJEB27496) and quantitative proteomics. In total 2290 proteins were identified with two unique peptides as requirement; of these, 1064 proteins were found to be quantifiable (identification in two out of three biological replicates and three out of five technical replicates). Relative quantification revealed that the majority of quantifiable proteins changed during maturation (693 out of 1064 proteins), sexual differences accounted for only 17 differentially expressed proteins, whereas lunar phase differences showed 261 differentially expressed proteins. This finding is in contrast to what was found on the transcriptome levels where differences in between the lunar phases only accounted for only 64 out of 52059 transcripts. To confirm this high degree of lunar regulated proteins a second proteome from immature animals at New moon and Free-running Full moon was undertaken. In this second set, we identified 2095 proteins of which 1671 were considered quantifiable. Of these 173 proteins showed significant differences between the New moon and the Free running full moon phase, thus confirming the previous results of a higher regulation on the protein compared to the transcript levels.
Project description:The main goal of the project was to analyze the effect of SNAIL transcription factor on microRNA expression profile in rhabdomyosarcoma (RMS) cells using the next generation sequencing. Differential expression of microRNAs between three groups was compared in RH30 alveolar RMS cells: WT (WT), shCTRL (modified with control shRNA vector) and shSNAIL (modified with shRNA against SNAIL). Different groups were compared to investigate the effect of SNAIL silencing on microRNA up- or downregulation.
Project description:The epithelial-to-mesenchymal transition (EMT) is a critical biological process in normal development and tumor progression. One of the EMT regulator, Snail is shown to suppress or activate its downstream genes to sustain migratory capacities while remodeling the tumor microenvironment. Identification of the Snail-regulated transcriptome through a robust sequencing technique will give a global direction for targeting Snail-driven malignancy.
Project description:Analysis of breast cancer survivors' gut microbiota after lifestyle intervention, during the COVID-19 lockdown, by 16S sequencing of fecal samples.
Project description:We found that mainstream cigarette smoking (4 cigarettes/day, 5 days/week for 2 weeks using Kentucky Research Cigarettes 3R4F) resulted in >20% decrease in the percentage of normal Paneth cell population in Atg16l1 T300A mice but showed minimal effect in wildtype littermate control mice, indicating that Atg16l1 T300A polymorphism confers sensitivity to cigarette smoking-induced Paneth cell damage. We performed cohousing experiments to test if Paneth cell phenotype is horizontally transmissible as is microbiota. Atg16l1 T300A and littermate controls that were exposed to cigarette smoking were used as microbiota donors, and these donor mice were exposed to smoking for 2 weeks prior to cohousing. Separate groups of Atg16l1 T300A and littermate controls that were not exposed to cigarette smoking were used as microbiota recipients. The microbiota recipients were co-housed with microbiota donors of the same genotype for 4 weeks, during this period the donors continued to be exposed to cigarette smoking. Cigarette smoking was performed using smoking chamber with the dosage and schedule as described above. At the end of the experiment, the fecal microbiota composition was analyzed by 16S rRNA sequencing.
Project description:This study is part of MD Anderson Cancer Center CRC Moon Shot. We used single cell RNAsequencing (scRNA-seq) to analyze the diversity of CRC.
Project description:ChIP-seq analysis of SNAIL binding sites in RH30 cells was performed to discover novel SNAIL binding sites in rhabdmyosarcoma cells.
